CITE-seq

Integration of single-cell multi-omic data with graph-based topic modelling

This paper introduces a graph-based topic modelling method for single-cell multi-omic data, showing improved performance in clustering and biological interpretation.

Partially Shared Multi-Modal Embedding Learns Holistic Representation of Cell State

APOLLO learns shared and modality-specific information from multi-modal single-cell data to improve understanding of cell state and regulatory mechanisms.

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

The paper introduces OneCell CUT&Tag, a single-cell multi-omics method that captures chromatin, transcriptome, and surface marker data, revealing epigenomic reprogramming during mammary gland basal-to-luminal transition.

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta

CryoZeta improves cryo-EM structure modeling by integrating density features with sequence data using a diffusion-based deep learning model, achieving higher accuracy than existing methods.

Programmable and Switchable RNA Scaffolds for Synthetic Condensate Engineering in Mammalian Cells

This paper develops programmable RNA scaffolds that form synthetic condensates in mammalian cells, showing that double-stranded RNA stems drive assembly and introducing an allosteric switch for reversible control.

Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood

The paper identifies TCR subsequence motifs associated with type 1 diabetes using deep learning and shows their enrichment in T1D individuals based on HLA risk alleles.

Antigen-specificity of clonally-enriched CD8+ T cells in multiple sclerosis

Paired CSF and blood scRNA/TCR-seq in treatment-naive MS shows a small set of expanded, cytotoxic CSF-enriched CD8+ clonotypes, two of which recognize EBV epitopes.

BiCLUM: Bilateral Contrastive Learning for Unpaired Single-Cell Multi-Omics Integration

BiCLUM integrates unpaired single-cell multi-omics data by aligning cell and feature spaces through bilateral contrastive learning, outperforming existing methods in visualization and quantitative metrics.

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The paper identifies 335 novel T cell receptor alleles in 47 pangenome reference individuals using the gAIRR Suite, significantly expanding the IMGT database.

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Single-cell and spatial maps of human coronary arteries identify FAP as a marker of SMC-derived modulated cells; an anti-FAP BiTE reduced plaque burden in mouse models.

Scalable TCR synthesis and screening enables antigen reactivity mapping in vitiligo

The paper introduces a scalable TCR synthesis and screening method, TCRAFT, to map antigen reactivity in vitiligo and pancreatic ductal adenocarcinoma.

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions

The paper presents OWHA, a 4D multimodal atlas of wound healing in mice, revealing a conserved Basal IV/SEMA3C circuit that coordinates repair, and shows its disruption in diabetic wounds.

Decoding the restriction of T cell receptors to human leukocyte antigen alleles using statistical learning

The paper uses statistical learning to decode T cell receptor associations with HLA alleles using a large dataset, identifying clonotypes linked to specific HLA alleles and infections.

IL-12R signaling promotes type 1 regulatory T cell specialization by sustaining T-bet

This study shows IL-12R signaling sustains T-bet in Treg cells, promoting type 1 specialization and enhancing suppressive function against Th1 responses.

A Fundamental Relationship between TCR Diversity, Repertoire Size and Systemic Clonal Expansion: Insights from 30,000 TCRβ Repertoires

The paper analyzes TCRβ repertoires from 30,000 individuals to show that TCR diversity is primarily determined by repertoire size and the frequency of the 1,000 most abundant clones, explaining 96% of variance in diversity.

Trained ILC2 prevent IL-17-associated lung injury during helminth infection through a serotonin-dependent mechanism

This study shows trained ILC2s prevent IL-17-driven lung injury during helminth re-infection via a serotonin-dependent mechanism, distinct from TH2 cells.

Regulatory T cells clonally expand and contribute to stromal cell function in fibrotic response to synthetic implants

The paper identifies Treg clonal expansion and immunosuppressive functions in fibrosis induced by synthetic implants, showing their role in modulating stromal cell behavior.

T cells use TNF and IFNγ for paracrine killing with target discrimination programmed by pathogen-derived factors

The paper shows T cells can kill target cells via TNF and IFNγ in a paracrine, perforin-independent manner, with pathogen-derived factors enabling selective elimination of infected cells.

Large generative mRNA language foundation model for efficient coding sequence generation and design with mRNA-GPT

The paper introduces mRNA-GPT, a generative mRNA language model trained on sequences from bacteria, eukaryotes, and archaea, showing improved translation efficiency and stability in mRNA design.

Statistical modelling of CDR3 sequences provides robust quality control for TCR repertoire datasets

The paper quantifies how V and J gene usage affects CDR3 length and amino acid composition in TCR repertoires and provides a quality control framework for TCR sequencing data.

Quantitative mapping of antigen specificity in adaptive immune repertoire embedding spaces

The paper quantitatively maps antigen specificity in immune repertoire embedding spaces, showing distinct regions for different antigen-specific sequences.

Unified Probabilistic Analysis of CyTOF: A Deep Generative Approach using CytoOne

CytoOne is a probabilistic framework for CyTOF data that integrates batch correction, differential analysis, and visualization, effectively modeling sparse and noisy data.

Repurposed endogenous virus-like vesicles mediate dendritic cell long-range antigen presentation and T cell activation for enhanced cancer vaccination

This paper shows that dendritic cells use virus-like vesicles to enhance antigen presentation and T cell activation, leading to improved cancer vaccination.

Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS

The paper identifies recipient stem-cell persistence and T-cell dysregulation as predictors of relapse after HSCT in AML/MDS by analyzing single-cell RNA and TCR sequencing data.

Peptide-MHC-targeted retroviruses enable in vivo expansion and gene delivery to tumor-specific T cells

This study develops pMHC-targeted retroviruses for in vivo gene delivery to tumor-specific T cells, enhancing their expansion and anti-tumor activity in mouse models.

MOFA-FLEX: A Factor Model Framework for Integrating Omics Data with Prior Knowledge

MOFA-FLEX is a flexible factor analysis framework that integrates multi-omics data with prior knowledge, improving robustness and disentangling variation in scRNA-seq and CITE-seq data.

CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations

CelLink integrates single-cell multi-omics data by addressing weak feature linkage and imbalanced cell populations, outperforming existing methods in imputation accuracy and cell subtype annotation.

Co-Stimulatory Blockade Prevents Intragraft Accrual of Class-Switched, Activated B Cells Despite Failing to Prevent T-Cell Mediated Rejection

The paper investigates the effects of co-stimulatory blockade on B cell accrual and T cell subsets during T-cell-mediated renal allograft rejection using single-cell RNA sequencing.

REPTRA: Mapping Immune T Cell Receptor Activity from Full Sequences with a Debiased Contrastive Loss

The paper introduces REPTRA, a contrastive learning model for TCR-epitope recognition using full TCR sequences and a debiased loss function, showing improved performance and highlighting the importance of CDR1 and CDR2.

TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations

TyCHE improves time-resolved lineage tracing by accounting for heterogeneous mutation rates, applied to memory B cells, germinal centers, gliomas, and bacterial infections.